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satta pushed a commit to branch master
in repository snp-sites.
commit 298cfae1360903f9d56510eff595fb7a3b27ad4b
Author: Sascha Steinbiss <sa...@debian.org>
Date: Tue Jun 13 12:09:49 2017 +0200
New upstream version 2.3.3
---
AUTHORS | 2 +-
Dockerfile | 19 +++++++++++++++++++
LICENSE | 4 ++++
VERSION | 2 +-
src/alignment-file.c | 2 +-
src/snp-sites.c | 14 ++++++++------
6 files changed, 34 insertions(+), 9 deletions(-)
diff --git a/AUTHORS b/AUTHORS
index 6d74363..bb6527c 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,3 +1,3 @@
Andrew J. Page <a...@sanger.ac.uk>
-Ben Taylor <b...@sanger.ac.uk>
+Ben Taylor <path-h...@sanger.ac.uk>
Jorge Soares <path-h...@sanger.ac.uk>
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..a1aeca3
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,19 @@
+#
+# From this base-image / starting-point
+#
+FROM debian:testing
+
+#
+# Authorship
+#
+MAINTAINER a...@sanger.ac.uk
+
+#
+# Pull in packages from testing
+#
+RUN apt-get update -qq
+
+#
+# Install Roary
+#
+RUN apt-get install snp-sites
diff --git a/LICENSE b/LICENSE
index c433dce..8050100 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2012 - 2016 by Genome Research Ltd.
+
+This is free software, licensed under:
+
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
diff --git a/VERSION b/VERSION
index f90b1af..0bee604 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.3.2
+2.3.3
diff --git a/src/alignment-file.c b/src/alignment-file.c
index b1d83d7..01b73b6 100644
--- a/src/alignment-file.c
+++ b/src/alignment-file.c
@@ -184,7 +184,7 @@ void detect_snps(char filename[], int pure_mode, int
output_monomorphic)
}
int current_snp_index = 0;
- snp_locations = calloc(number_of_snps, sizeof(int));
+ snp_locations = calloc(number_of_snps +1, sizeof(int));
for(i = 0; i < length_of_genome; i++)
{
if(first_sequence[i] == '>' || (output_monomorphic && first_sequence[i]
!= '#'))
diff --git a/src/snp-sites.c b/src/snp-sites.c
index 8ce28aa..0f56224 100644
--- a/src/snp-sites.c
+++ b/src/snp-sites.c
@@ -27,6 +27,8 @@
#include "phylib-of-snp-sites.h"
#include "fasta-of-snp-sites.h"
+char ** bases_for_snps;
+
static int generate_snp_sites_generic(char filename[],
int output_multi_fasta_file,
int output_vcf_file,
@@ -37,20 +39,20 @@ static int generate_snp_sites_generic(char filename[],
int i;
detect_snps(filename, pure_mode, output_monomorphic);
- char* bases_for_snps[get_number_of_snps()];
-
+ bases_for_snps = calloc(get_number_of_snps()+1, sizeof(char*));
+
for(i = 0; i < get_number_of_snps(); i++)
{
- bases_for_snps[i] = calloc(get_number_of_samples()+1
,sizeof(char));
+ bases_for_snps[i] = calloc(get_number_of_samples()+1,
sizeof(char));
}
-
+
get_bases_for_each_snp(filename, bases_for_snps);
-
+
char output_filename_base[FILENAME_MAX];
char filename_without_directory[FILENAME_MAX];
strip_directory_from_filename(filename, filename_without_directory);
strncpy(output_filename_base, filename_without_directory, FILENAME_MAX);
-
+
if(output_filename != NULL && *output_filename != '\0')
{
strncpy(output_filename_base, output_filename, FILENAME_MAX);
--
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